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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp

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trunk/src/integrators/RNEMD.cpp (file contents), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1854 by gezelter, Thu Mar 28 20:54:06 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
19	<	*    notice, this list of conditions and the following disclaimer.
20	<	*
21	<	* 3. Redistributions in binary form must reproduce the above copyright
22	<	*    notice, this list of conditions and the following disclaimer in the
23	<	*    documentation and/or other materials provided with the
24	<	*    distribution.
25	<	*
26	<	* This software is provided "AS IS," without a warranty of any
27	<	* kind. All express or implied conditions, representations and
28	<	* warranties, including any implied warranty of merchantability,
29	<	* fitness for a particular purpose or non-infringement, are hereby
30	<	* excluded.  The University of Notre Dame and its licensors shall not
31	<	* be liable for any damages suffered by licensee as a result of
32	<	* using, modifying or distributing the software or its
33	<	* derivatives. In no event will the University of Notre Dame or its
34	<	* licensors be liable for any lost revenue, profit or data, or for
35	<	* direct, indirect, special, consequential, incidental or punitive
36	<	* damages, however caused and regardless of the theory of liability,
37	<	* arising out of the use of or inability to use software, even if the
38	<	* University of Notre Dame has been advised of the possibility of
39	<	* such damages.
40	<	*/
41	<
42	<	#include "integrators/RNEMD.hpp"
43	<	#include "math/SquareMatrix3.hpp"
44	<	#include "primitives/Molecule.hpp"
45	<	#include "primitives/StuntDouble.hpp"
46	<
47	<	#ifndef IS_MPI
48	<	#include "math/SeqRandNumGen.hpp"
49	<	#else
50	<	#include "math/ParallelRandNumGen.hpp"
51	<	#endif
52	<
53	<	/* Remove me after testing*/
54	<	/*
55	<	#include <cstdio>
56	<	#include <iostream>
57	<	*/
58	<	/*End remove me*/
59	<
60	<	namespace oopse {
61	<
62	<	RNEMD::RNEMD(SimInfo* info) : info_(info) {
63	<
64	<	int seedValue;
65	<	Globals * simParams = info->getSimParams();
66	<
67	<	stringToEnumMap_["Kinetic"] = rnemdKinetic;
68	<	stringToEnumMap_["Px"] = rnemdPx;
69	<	stringToEnumMap_["Py"] = rnemdPy;
70	<	stringToEnumMap_["Pz"] = rnemdPz;
71	<	stringToEnumMap_["Unknown"] = rnemdUnknown;
72	<
73	<	const std::string st = simParams->getRNEMD_swapType();
74	<
75	<	std::map<std::string, RNEMDTypeEnum>::iterator i;
76	<	i = stringToEnumMap_.find(st);
77	<	rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
78	<
79	<
80	<	set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
81	<	set_RNEMD_nBins(simParams->getRNEMD_nBins());
82	<	exchangeSum_ = 0.0;
83	<
84	<	#ifndef IS_MPI
85	<	if (simParams->haveSeed()) {
86	<	seedValue = simParams->getSeed();
87	<	randNumGen_ = new SeqRandNumGen(seedValue);
88	<	}else {
89	<	randNumGen_ = new SeqRandNumGen();
90	<	}
91	<	#else
92	<	if (simParams->haveSeed()) {
93	<	seedValue = simParams->getSeed();
94	<	randNumGen_ = new ParallelRandNumGen(seedValue);
95	<	}else {
96	<	randNumGen_ = new ParallelRandNumGen();
97	<	}
98	<	#endif
99	<	}
100	<
101	<	RNEMD::~RNEMD() {
102	<	delete randNumGen_;
103	<	}
104	<
105	<	void RNEMD::doSwap() {
106	<	std::cerr << "in RNEMD!\n";
107	<	std::cerr << "nBins = " << nBins_ << "\n";
108	<	std::cerr << "swapTime = " << swapTime_ << "\n";
109	<	std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
110	<	std::cerr << "swapType = " << rnemdType_ << "\n";
111	<	}
112	<	}
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	#include <cmath>
43	>	#include <sstream>
44	>	#include <string>
45	>
46	>	#include "rnemd/RNEMD.hpp"
47	>	#include "math/Vector3.hpp"
48	>	#include "math/Vector.hpp"
49	>	#include "math/SquareMatrix3.hpp"
50	>	#include "math/Polynomial.hpp"
51	>	#include "primitives/Molecule.hpp"
52	>	#include "primitives/StuntDouble.hpp"
53	>	#include "utils/PhysicalConstants.hpp"
54	>	#include "utils/Tuple.hpp"
55	>	#include "brains/Thermo.hpp"
56	>	#include "math/ConvexHull.hpp"
57	>	#ifdef IS_MPI
58	>	#include <mpi.h>
59	>	#endif
60	>
61	>	#ifdef _MSC_VER
62	>	#define isnan(x) _isnan((x))
63	>	#define isinf(x) (!_finite(x) && !_isnan(x))
64	>	#endif
65	>
66	>	#define HONKING_LARGE_VALUE 1.0e10
67	>
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	>	evaluatorA_(info), seleManA_(info),
73	>	commonA_(info), evaluatorB_(info),
74	>	seleManB_(info), commonB_(info),
75	>	usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
76	>
77	>	trialCount_ = 0;
78	>	failTrialCount_ = 0;
79	>	failRootCount_ = 0;
80	>
81	>	Globals* simParams = info->getSimParams();
82	>	RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
83	>
84	>	doRNEMD_ = rnemdParams->getUseRNEMD();
85	>	if (!doRNEMD_) return;
86	>
87	>	stringToMethod_["Swap"]  = rnemdSwap;
88	>	stringToMethod_["NIVS"]  = rnemdNIVS;
89	>	stringToMethod_["VSS"]   = rnemdVSS;
90	>
91	>	stringToFluxType_["KE"]  = rnemdKE;
92	>	stringToFluxType_["Px"]  = rnemdPx;
93	>	stringToFluxType_["Py"]  = rnemdPy;
94	>	stringToFluxType_["Pz"]  = rnemdPz;
95	>	stringToFluxType_["Pvector"]  = rnemdPvector;
96	>	stringToFluxType_["Lx"]  = rnemdLx;
97	>	stringToFluxType_["Ly"]  = rnemdLy;
98	>	stringToFluxType_["Lz"]  = rnemdLz;
99	>	stringToFluxType_["Lvector"]  = rnemdLvector;
100	>	stringToFluxType_["KE+Px"]  = rnemdKePx;
101	>	stringToFluxType_["KE+Py"]  = rnemdKePy;
102	>	stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
103	>	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
104	>	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
105	>	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
106	>	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
107	>
108	>	runTime_ = simParams->getRunTime();
109	>	statusTime_ = simParams->getStatusTime();
110	>
111	>	const string methStr = rnemdParams->getMethod();
112	>	bool hasFluxType = rnemdParams->haveFluxType();
113	>
114	>	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
115	>
116	>	string fluxStr;
117	>	if (hasFluxType) {
118	>	fluxStr = rnemdParams->getFluxType();
119	>	} else {
120	>	sprintf(painCave.errMsg,
121	>	"RNEMD: No fluxType was set in the md file.  This parameter,\n"
122	>	"\twhich must be one of the following values:\n"
123	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
124	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
125	>	"\tmust be set to use RNEMD\n");
126	>	painCave.isFatal = 1;
127	>	painCave.severity = OPENMD_ERROR;
128	>	simError();
129	>	}
130	>
131	>	bool hasKineticFlux = rnemdParams->haveKineticFlux();
132	>	bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
133	>	bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
134	>	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
135	>	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
136	>	hasSelectionA_ = rnemdParams->haveSelectionA();
137	>	hasSelectionB_ = rnemdParams->haveSelectionB();
138	>	bool hasSlabWidth = rnemdParams->haveSlabWidth();
139	>	bool hasSlabACenter = rnemdParams->haveSlabACenter();
140	>	bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
141	>	bool hasSphereARadius = rnemdParams->haveSphereARadius();
142	>	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
143	>	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
144	>	bool hasOutputFileName = rnemdParams->haveOutputFileName();
145	>	bool hasOutputFields = rnemdParams->haveOutputFields();
146	>
147	>	map<string, RNEMDMethod>::iterator i;
148	>	i = stringToMethod_.find(methStr);
149	>	if (i != stringToMethod_.end())
150	>	rnemdMethod_ = i->second;
151	>	else {
152	>	sprintf(painCave.errMsg,
153	>	"RNEMD: The current method,\n"
154	>	"\t\t%s is not one of the recognized\n"
155	>	"\texchange methods: Swap, NIVS, or VSS\n",
156	>	methStr.c_str());
157	>	painCave.isFatal = 1;
158	>	painCave.severity = OPENMD_ERROR;
159	>	simError();
160	>	}
161	>
162	>	map<string, RNEMDFluxType>::iterator j;
163	>	j = stringToFluxType_.find(fluxStr);
164	>	if (j != stringToFluxType_.end())
165	>	rnemdFluxType_ = j->second;
166	>	else {
167	>	sprintf(painCave.errMsg,
168	>	"RNEMD: The current fluxType,\n"
169	>	"\t\t%s\n"
170	>	"\tis not one of the recognized flux types.\n",
171	>	fluxStr.c_str());
172	>	painCave.isFatal = 1;
173	>	painCave.severity = OPENMD_ERROR;
174	>	simError();
175	>	}
176	>
177	>	bool methodFluxMismatch = false;
178	>	bool hasCorrectFlux = false;
179	>	switch(rnemdMethod_) {
180	>	case rnemdSwap:
181	>	switch (rnemdFluxType_) {
182	>	case rnemdKE:
183	>	hasCorrectFlux = hasKineticFlux;
184	>	break;
185	>	case rnemdPx:
186	>	case rnemdPy:
187	>	case rnemdPz:
188	>	hasCorrectFlux = hasMomentumFlux;
189	>	break;
190	>	default :
191	>	methodFluxMismatch = true;
192	>	break;
193	>	}
194	>	break;
195	>	case rnemdNIVS:
196	>	switch (rnemdFluxType_) {
197	>	case rnemdKE:
198	>	case rnemdRotKE:
199	>	case rnemdFullKE:
200	>	hasCorrectFlux = hasKineticFlux;
201	>	break;
202	>	case rnemdPx:
203	>	case rnemdPy:
204	>	case rnemdPz:
205	>	hasCorrectFlux = hasMomentumFlux;
206	>	break;
207	>	case rnemdKePx:
208	>	case rnemdKePy:
209	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
210	>	break;
211	>	default:
212	>	methodFluxMismatch = true;
213	>	break;
214	>	}
215	>	break;
216	>	case rnemdVSS:
217	>	switch (rnemdFluxType_) {
218	>	case rnemdKE:
219	>	case rnemdRotKE:
220	>	case rnemdFullKE:
221	>	hasCorrectFlux = hasKineticFlux;
222	>	break;
223	>	case rnemdPx:
224	>	case rnemdPy:
225	>	case rnemdPz:
226	>	hasCorrectFlux = hasMomentumFlux;
227	>	break;
228	>	case rnemdLx:
229	>	case rnemdLy:
230	>	case rnemdLz:
231	>	hasCorrectFlux = hasAngularMomentumFlux;
232	>	break;
233	>	case rnemdPvector:
234	>	hasCorrectFlux = hasMomentumFluxVector;
235	>	break;
236	>	case rnemdLvector:
237	>	hasCorrectFlux = hasAngularMomentumFluxVector;
238	>	break;
239	>	case rnemdKePx:
240	>	case rnemdKePy:
241	>	hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
242	>	break;
243	>	case rnemdKeLx:
244	>	case rnemdKeLy:
245	>	case rnemdKeLz:
246	>	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
247	>	break;
248	>	case rnemdKePvector:
249	>	hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
250	>	break;
251	>	case rnemdKeLvector:
252	>	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
253	>	break;
254	>	default:
255	>	methodFluxMismatch = true;
256	>	break;
257	>	}
258	>	default:
259	>	break;
260	>	}
261	>
262	>	if (methodFluxMismatch) {
263	>	sprintf(painCave.errMsg,
264	>	"RNEMD: The current method,\n"
265	>	"\t\t%s\n"
266	>	"\tcannot be used with the current flux type, %s\n",
267	>	methStr.c_str(), fluxStr.c_str());
268	>	painCave.isFatal = 1;
269	>	painCave.severity = OPENMD_ERROR;
270	>	simError();
271	>	}
272	>	if (!hasCorrectFlux) {
273	>	sprintf(painCave.errMsg,
274	>	"RNEMD: The current method, %s, and flux type, %s,\n"
275	>	"\tdid not have the correct flux value specified. Options\n"
276	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
277	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
278	>	methStr.c_str(), fluxStr.c_str());
279	>	painCave.isFatal = 1;
280	>	painCave.severity = OPENMD_ERROR;
281	>	simError();
282	>	}
283	>
284	>	if (hasKineticFlux) {
285	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
286	>	// into  amu / fs^3:
287	>	kineticFlux_ = rnemdParams->getKineticFlux()
288	>	* PhysicalConstants::energyConvert;
289	>	} else {
290	>	kineticFlux_ = 0.0;
291	>	}
292	>	if (hasMomentumFluxVector) {
293	>	momentumFluxVector_ = rnemdParams->getMomentumFluxVector();
294	>	} else {
295	>	momentumFluxVector_ = V3Zero;
296	>	if (hasMomentumFlux) {
297	>	RealType momentumFlux = rnemdParams->getMomentumFlux();
298	>	switch (rnemdFluxType_) {
299	>	case rnemdPx:
300	>	momentumFluxVector_.x() = momentumFlux;
301	>	break;
302	>	case rnemdPy:
303	>	momentumFluxVector_.y() = momentumFlux;
304	>	break;
305	>	case rnemdPz:
306	>	momentumFluxVector_.z() = momentumFlux;
307	>	break;
308	>	case rnemdKePx:
309	>	momentumFluxVector_.x() = momentumFlux;
310	>	break;
311	>	case rnemdKePy:
312	>	momentumFluxVector_.y() = momentumFlux;
313	>	break;
314	>	default:
315	>	break;
316	>	}
317	>	}
318	>	if (hasAngularMomentumFluxVector) {
319	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
320	>	} else {
321	>	angularMomentumFluxVector_ = V3Zero;
322	>	if (hasAngularMomentumFlux) {
323	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
324	>	switch (rnemdFluxType_) {
325	>	case rnemdLx:
326	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
327	>	break;
328	>	case rnemdLy:
329	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
330	>	break;
331	>	case rnemdLz:
332	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
333	>	break;
334	>	case rnemdKeLx:
335	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
336	>	break;
337	>	case rnemdKeLy:
338	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
339	>	break;
340	>	case rnemdKeLz:
341	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
342	>	break;
343	>	default:
344	>	break;
345	>	}
346	>	}
347	>	}
348	>
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351	>	} else {
352	>	coordinateOrigin_ = V3Zero;
353	>	}
354	>
355	>	// do some sanity checking
356	>
357	>	int selectionCount = seleMan_.getSelectionCount();
358	>
359	>	int nIntegrable = info->getNGlobalIntegrableObjects();
360	>
361	>	if (selectionCount > nIntegrable) {
362	>	sprintf(painCave.errMsg,
363	>	"RNEMD: The current objectSelection,\n"
364	>	"\t\t%s\n"
365	>	"\thas resulted in %d selected objects.  However,\n"
366	>	"\tthe total number of integrable objects in the system\n"
367	>	"\tis only %d.  This is almost certainly not what you want\n"
368	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
369	>	"\tselector in the selection script!\n",
370	>	rnemdObjectSelection_.c_str(),
371	>	selectionCount, nIntegrable);
372	>	painCave.isFatal = 0;
373	>	painCave.severity = OPENMD_WARNING;
374	>	simError();
375	>	}
376	>
377	>	areaAccumulator_ = new Accumulator();
378	>
379	>	nBins_ = rnemdParams->getOutputBins();
380	>	binWidth_ = rnemdParams->getOutputBinWidth();
381	>
382	>	data_.resize(RNEMD::ENDINDEX);
383	>	OutputData z;
384	>	z.units =  "Angstroms";
385	>	z.title =  "Z";
386	>	z.dataType = "RealType";
387	>	z.accumulator.reserve(nBins_);
388	>	for (int i = 0; i < nBins_; i++)
389	>	z.accumulator.push_back( new Accumulator() );
390	>	data_[Z] = z;
391	>	outputMap_["Z"] =  Z;
392	>
393	>	OutputData r;
394	>	r.units =  "Angstroms";
395	>	r.title =  "R";
396	>	r.dataType = "RealType";
397	>	r.accumulator.reserve(nBins_);
398	>	for (int i = 0; i < nBins_; i++)
399	>	r.accumulator.push_back( new Accumulator() );
400	>	data_[R] = r;
401	>	outputMap_["R"] =  R;
402	>
403	>	OutputData temperature;
404	>	temperature.units =  "K";
405	>	temperature.title =  "Temperature";
406	>	temperature.dataType = "RealType";
407	>	temperature.accumulator.reserve(nBins_);
408	>	for (int i = 0; i < nBins_; i++)
409	>	temperature.accumulator.push_back( new Accumulator() );
410	>	data_[TEMPERATURE] = temperature;
411	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
412	>
413	>	OutputData velocity;
414	>	velocity.units = "angstroms/fs";
415	>	velocity.title =  "Velocity";
416	>	velocity.dataType = "Vector3d";
417	>	velocity.accumulator.reserve(nBins_);
418	>	for (int i = 0; i < nBins_; i++)
419	>	velocity.accumulator.push_back( new VectorAccumulator() );
420	>	data_[VELOCITY] = velocity;
421	>	outputMap_["VELOCITY"] = VELOCITY;
422	>
423	>	OutputData density;
424	>	density.units =  "g cm^-3";
425	>	density.title =  "Density";
426	>	density.dataType = "RealType";
427	>	density.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	density.accumulator.push_back( new Accumulator() );
430	>	data_[DENSITY] = density;
431	>	outputMap_["DENSITY"] =  DENSITY;
432	>
433	>	if (hasOutputFields) {
434	>	parseOutputFileFormat(rnemdParams->getOutputFields());
435	>	} else {
436	>	if (usePeriodicBoundaryConditions_)
437	>	outputMask_.set(Z);
438	>	else
439	>	outputMask_.set(R);
440	>	switch (rnemdFluxType_) {
441	>	case rnemdKE:
442	>	case rnemdRotKE:
443	>	case rnemdFullKE:
444	>	outputMask_.set(TEMPERATURE);
445	>	break;
446	>	case rnemdPx:
447	>	case rnemdPy:
448	>	outputMask_.set(VELOCITY);
449	>	break;
450	>	case rnemdPz:
451	>	case rnemdPvector:
452	>	outputMask_.set(VELOCITY);
453	>	outputMask_.set(DENSITY);
454	>	break;
455	>	case rnemdLx:
456	>	case rnemdLy:
457	>	case rnemdLz:
458	>	case rnemdLvector:
459	>	outputMask_.set(ANGULARVELOCITY);
460	>	break;
461	>	case rnemdKeLx:
462	>	case rnemdKeLy:
463	>	case rnemdKeLz:
464	>	case rnemdKeLvector:
465	>	outputMask_.set(TEMPERATURE);
466	>	outputMask_.set(ANGULARVELOCITY);
467	>	break;
468	>	case rnemdKePx:
469	>	case rnemdKePy:
470	>	outputMask_.set(TEMPERATURE);
471	>	outputMask_.set(VELOCITY);
472	>	break;
473	>	case rnemdKePvector:
474	>	outputMask_.set(TEMPERATURE);
475	>	outputMask_.set(VELOCITY);
476	>	outputMask_.set(DENSITY);
477	>	break;
478	>	default:
479	>	break;
480	>	}
481	>	}
482	>
483	>	if (hasOutputFileName) {
484	>	rnemdFileName_ = rnemdParams->getOutputFileName();
485	>	} else {
486	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
487	>	}
488	>
489	>	exchangeTime_ = rnemdParams->getExchangeTime();
490	>
491	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
492	>	// total exchange sums are zeroed out at the beginning:
493	>
494	>	kineticExchange_ = 0.0;
495	>	momentumExchange_ = V3Zero;
496	>	angularMomentumExchange_ = V3Zero;
497	>
498	>	std::ostringstream selectionAstream;
499	>	std::ostringstream selectionBstream;
500	>
501	>	if (hasSelectionA_) {
502	>	selectionA_ = rnemdParams->getSelectionA();
503	>	} else {
504	>	if (usePeriodicBoundaryConditions_) {
505	>	Mat3x3d hmat = currentSnap_->getHmat();
506	>
507	>	if (hasSlabWidth)
508	>	slabWidth_ = rnemdParams->getSlabWidth();
509	>	else
510	>	slabWidth_ = hmat(2,2) / 10.0;
511	>
512	>	if (hasSlabACenter)
513	>	slabACenter_ = rnemdParams->getSlabACenter();
514	>	else
515	>	slabACenter_ = 0.0;
516	>
517	>	selectionAstream << "select wrappedz > "
518	>	<< slabACenter_ - 0.5*slabWidth_
519	>	<<  " && wrappedz < "
520	>	<< slabACenter_ + 0.5*slabWidth_;
521	>	selectionA_ = selectionAstream.str();
522	>	} else {
523	>	if (hasSphereARadius)
524	>	sphereARadius_ = rnemdParams->getSphereARadius();
525	>	else {
526	>	// use an initial guess to the size of the inner slab to be 1/10 the
527	>	// radius of an approximately spherical hull:
528	>	Thermo thermo(info);
529	>	RealType hVol = thermo.getHullVolume();
530	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
531	>	}
532	>	selectionAstream << "select r < " << sphereARadius_;
533	>	selectionA_ = selectionAstream.str();
534	>	}
535	>	}
536	>
537	>	if (hasSelectionB_) {
538	>	selectionB_ = rnemdParams->getSelectionB();
539	>	} else {
540	>	if (usePeriodicBoundaryConditions_) {
541	>	Mat3x3d hmat = currentSnap_->getHmat();
542	>
543	>	if (hasSlabWidth)
544	>	slabWidth_ = rnemdParams->getSlabWidth();
545	>	else
546	>	slabWidth_ = hmat(2,2) / 10.0;
547	>
548	>	if (hasSlabBCenter)
549	>	slabBCenter_ = rnemdParams->getSlabACenter();
550	>	else
551	>	slabBCenter_ = hmat(2,2) / 2.0;
552	>
553	>	selectionBstream << "select wrappedz > "
554	>	<< slabBCenter_ - 0.5*slabWidth_
555	>	<<  " && wrappedz < "
556	>	<< slabBCenter_ + 0.5*slabWidth_;
557	>	selectionB_ = selectionBstream.str();
558	>	} else {
559	>	if (hasSphereBRadius_) {
560	>	sphereBRadius_ = rnemdParams->getSphereBRadius();
561	>	selectionBstream << "select r > " << sphereBRadius_;
562	>	selectionB_ = selectionBstream.str();
563	>	} else {
564	>	selectionB_ = "select hull";
565	>	hasSelectionB_ = true;
566	>	}
567	>	}
568	>	}
569	>	}
570	>	// object evaluator:
571	>	evaluator_.loadScriptString(rnemdObjectSelection_);
572	>	seleMan_.setSelectionSet(evaluator_.evaluate());
573	>
574	>	evaluatorA_.loadScriptString(selectionA_);
575	>	evaluatorB_.loadScriptString(selectionB_);
576	>
577	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
578	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
579	>
580	>	commonA_ = seleManA_ & seleMan_;
581	>	commonB_ = seleManB_ & seleMan_;
582	>	}
583	>
584	>
585	>	RNEMD::~RNEMD() {
586	>	if (!doRNEMD_) return;
587	>	#ifdef IS_MPI
588	>	if (worldRank == 0) {
589	>	#endif
590	>
591	>	writeOutputFile();
592	>
593	>	rnemdFile_.close();
594	>
595	>	#ifdef IS_MPI
596	>	}
597	>	#endif
598	>	}
599	>
600	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
601	>	if (!doRNEMD_) return;
602	>	int selei;
603	>	int selej;
604	>
605	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
606	>	Mat3x3d hmat = currentSnap_->getHmat();
607	>
608	>	StuntDouble* sd;
609	>
610	>	RealType min_val;
611	>	bool min_found = false;
612	>	StuntDouble* min_sd;
613	>
614	>	RealType max_val;
615	>	bool max_found = false;
616	>	StuntDouble* max_sd;
617	>
618	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
619	>	sd = seleManA_.nextSelected(selei)) {
620	>
621	>	Vector3d pos = sd->getPos();
622	>
623	>	// wrap the stuntdouble's position back into the box:
624	>
625	>	if (usePeriodicBoundaryConditions_)
626	>	currentSnap_->wrapVector(pos);
627	>
628	>	RealType mass = sd->getMass();
629	>	Vector3d vel = sd->getVel();
630	>	RealType value;
631	>
632	>	switch(rnemdFluxType_) {
633	>	case rnemdKE :
634	>
635	>	value = mass * vel.lengthSquare();
636	>
637	>	if (sd->isDirectional()) {
638	>	Vector3d angMom = sd->getJ();
639	>	Mat3x3d I = sd->getI();
640	>
641	>	if (sd->isLinear()) {
642	>	int i = sd->linearAxis();
643	>	int j = (i + 1) % 3;
644	>	int k = (i + 2) % 3;
645	>	value += angMom[j] * angMom[j] / I(j, j) +
646	>	angMom[k] * angMom[k] / I(k, k);
647	>	} else {
648	>	value += angMom[0]*angMom[0]/I(0, 0)
649	>	+ angMom[1]*angMom[1]/I(1, 1)
650	>	+ angMom[2]*angMom[2]/I(2, 2);
651	>	}
652	>	} //angular momenta exchange enabled
653	>	value *= 0.5;
654	>	break;
655	>	case rnemdPx :
656	>	value = mass * vel[0];
657	>	break;
658	>	case rnemdPy :
659	>	value = mass * vel[1];
660	>	break;
661	>	case rnemdPz :
662	>	value = mass * vel[2];
663	>	break;
664	>	default :
665	>	break;
666	>	}
667	>	if (!max_found) {
668	>	max_val = value;
669	>	max_sd = sd;
670	>	max_found = true;
671	>	} else {
672	>	if (max_val < value) {
673	>	max_val = value;
674	>	max_sd = sd;
675	>	}
676	>	}
677	>	}
678	>
679	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
680	>	sd = seleManB_.nextSelected(selej)) {
681	>
682	>	Vector3d pos = sd->getPos();
683	>
684	>	// wrap the stuntdouble's position back into the box:
685	>
686	>	if (usePeriodicBoundaryConditions_)
687	>	currentSnap_->wrapVector(pos);
688	>
689	>	RealType mass = sd->getMass();
690	>	Vector3d vel = sd->getVel();
691	>	RealType value;
692	>
693	>	switch(rnemdFluxType_) {
694	>	case rnemdKE :
695	>
696	>	value = mass * vel.lengthSquare();
697	>
698	>	if (sd->isDirectional()) {
699	>	Vector3d angMom = sd->getJ();
700	>	Mat3x3d I = sd->getI();
701	>
702	>	if (sd->isLinear()) {
703	>	int i = sd->linearAxis();
704	>	int j = (i + 1) % 3;
705	>	int k = (i + 2) % 3;
706	>	value += angMom[j] * angMom[j] / I(j, j) +
707	>	angMom[k] * angMom[k] / I(k, k);
708	>	} else {
709	>	value += angMom[0]*angMom[0]/I(0, 0)
710	>	+ angMom[1]*angMom[1]/I(1, 1)
711	>	+ angMom[2]*angMom[2]/I(2, 2);
712	>	}
713	>	} //angular momenta exchange enabled
714	>	value *= 0.5;
715	>	break;
716	>	case rnemdPx :
717	>	value = mass * vel[0];
718	>	break;
719	>	case rnemdPy :
720	>	value = mass * vel[1];
721	>	break;
722	>	case rnemdPz :
723	>	value = mass * vel[2];
724	>	break;
725	>	default :
726	>	break;
727	>	}
728	>
729	>	if (!min_found) {
730	>	min_val = value;
731	>	min_sd = sd;
732	>	min_found = true;
733	>	} else {
734	>	if (min_val > value) {
735	>	min_val = value;
736	>	min_sd = sd;
737	>	}
738	>	}
739	>	}
740	>
741	>	#ifdef IS_MPI
742	>	int worldRank = MPI::COMM_WORLD.Get_rank();
743	>
744	>	bool my_min_found = min_found;
745	>	bool my_max_found = max_found;
746	>
747	>	// Even if we didn't find a minimum, did someone else?
748	>	MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 1, MPI::BOOL, MPI::LOR);
749	>	// Even if we didn't find a maximum, did someone else?
750	>	MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 1, MPI::BOOL, MPI::LOR);
751	>	#endif
752	>
753	>	if (max_found && min_found) {
754	>
755	>	#ifdef IS_MPI
756	>	struct {
757	>	RealType val;
758	>	int rank;
759	>	} max_vals, min_vals;
760	>
761	>	if (my_min_found) {
762	>	min_vals.val = min_val;
763	>	} else {
764	>	min_vals.val = HONKING_LARGE_VALUE;
765	>	}
766	>	min_vals.rank = worldRank;
767	>
768	>	// Who had the minimum?
769	>	MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
770	>	1, MPI::REALTYPE_INT, MPI::MINLOC);
771	>	min_val = min_vals.val;
772	>
773	>	if (my_max_found) {
774	>	max_vals.val = max_val;
775	>	} else {
776	>	max_vals.val = -HONKING_LARGE_VALUE;
777	>	}
778	>	max_vals.rank = worldRank;
779	>
780	>	// Who had the maximum?
781	>	MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
782	>	1, MPI::REALTYPE_INT, MPI::MAXLOC);
783	>	max_val = max_vals.val;
784	>	#endif
785	>
786	>	if (min_val < max_val) {
787	>
788	>	#ifdef IS_MPI
789	>	if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
790	>	// I have both maximum and minimum, so proceed like a single
791	>	// processor version:
792	>	#endif
793	>
794	>	Vector3d min_vel = min_sd->getVel();
795	>	Vector3d max_vel = max_sd->getVel();
796	>	RealType temp_vel;
797	>
798	>	switch(rnemdFluxType_) {
799	>	case rnemdKE :
800	>	min_sd->setVel(max_vel);
801	>	max_sd->setVel(min_vel);
802	>	if (min_sd->isDirectional() && max_sd->isDirectional()) {
803	>	Vector3d min_angMom = min_sd->getJ();
804	>	Vector3d max_angMom = max_sd->getJ();
805	>	min_sd->setJ(max_angMom);
806	>	max_sd->setJ(min_angMom);
807	>	}//angular momenta exchange enabled
808	>	//assumes same rigid body identity
809	>	break;
810	>	case rnemdPx :
811	>	temp_vel = min_vel.x();
812	>	min_vel.x() = max_vel.x();
813	>	max_vel.x() = temp_vel;
814	>	min_sd->setVel(min_vel);
815	>	max_sd->setVel(max_vel);
816	>	break;
817	>	case rnemdPy :
818	>	temp_vel = min_vel.y();
819	>	min_vel.y() = max_vel.y();
820	>	max_vel.y() = temp_vel;
821	>	min_sd->setVel(min_vel);
822	>	max_sd->setVel(max_vel);
823	>	break;
824	>	case rnemdPz :
825	>	temp_vel = min_vel.z();
826	>	min_vel.z() = max_vel.z();
827	>	max_vel.z() = temp_vel;
828	>	min_sd->setVel(min_vel);
829	>	max_sd->setVel(max_vel);
830	>	break;
831	>	default :
832	>	break;
833	>	}
834	>
835	>	#ifdef IS_MPI
836	>	// the rest of the cases only apply in parallel simulations:
837	>	} else if (max_vals.rank == worldRank) {
838	>	// I had the max, but not the minimum
839	>
840	>	Vector3d min_vel;
841	>	Vector3d max_vel = max_sd->getVel();
842	>	MPI::Status status;
843	>
844	>	// point-to-point swap of the velocity vector
845	>	MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
846	>	min_vals.rank, 0,
847	>	min_vel.getArrayPointer(), 3, MPI::REALTYPE,
848	>	min_vals.rank, 0, status);
849	>
850	>	switch(rnemdFluxType_) {
851	>	case rnemdKE :
852	>	max_sd->setVel(min_vel);
853	>	//angular momenta exchange enabled
854	>	if (max_sd->isDirectional()) {
855	>	Vector3d min_angMom;
856	>	Vector3d max_angMom = max_sd->getJ();
857	>
858	>	// point-to-point swap of the angular momentum vector
859	>	MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
860	>	MPI::REALTYPE, min_vals.rank, 1,
861	>	min_angMom.getArrayPointer(), 3,
862	>	MPI::REALTYPE, min_vals.rank, 1,
863	>	status);
864	>
865	>	max_sd->setJ(min_angMom);
866	>	}
867	>	break;
868	>	case rnemdPx :
869	>	max_vel.x() = min_vel.x();
870	>	max_sd->setVel(max_vel);
871	>	break;
872	>	case rnemdPy :
873	>	max_vel.y() = min_vel.y();
874	>	max_sd->setVel(max_vel);
875	>	break;
876	>	case rnemdPz :
877	>	max_vel.z() = min_vel.z();
878	>	max_sd->setVel(max_vel);
879	>	break;
880	>	default :
881	>	break;
882	>	}
883	>	} else if (min_vals.rank == worldRank) {
884	>	// I had the minimum but not the maximum:
885	>
886	>	Vector3d max_vel;
887	>	Vector3d min_vel = min_sd->getVel();
888	>	MPI::Status status;
889	>
890	>	// point-to-point swap of the velocity vector
891	>	MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
892	>	max_vals.rank, 0,
893	>	max_vel.getArrayPointer(), 3, MPI::REALTYPE,
894	>	max_vals.rank, 0, status);
895	>
896	>	switch(rnemdFluxType_) {
897	>	case rnemdKE :
898	>	min_sd->setVel(max_vel);
899	>	//angular momenta exchange enabled
900	>	if (min_sd->isDirectional()) {
901	>	Vector3d min_angMom = min_sd->getJ();
902	>	Vector3d max_angMom;
903	>
904	>	// point-to-point swap of the angular momentum vector
905	>	MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
906	>	MPI::REALTYPE, max_vals.rank, 1,
907	>	max_angMom.getArrayPointer(), 3,
908	>	MPI::REALTYPE, max_vals.rank, 1,
909	>	status);
910	>
911	>	min_sd->setJ(max_angMom);
912	>	}
913	>	break;
914	>	case rnemdPx :
915	>	min_vel.x() = max_vel.x();
916	>	min_sd->setVel(min_vel);
917	>	break;
918	>	case rnemdPy :
919	>	min_vel.y() = max_vel.y();
920	>	min_sd->setVel(min_vel);
921	>	break;
922	>	case rnemdPz :
923	>	min_vel.z() = max_vel.z();
924	>	min_sd->setVel(min_vel);
925	>	break;
926	>	default :
927	>	break;
928	>	}
929	>	}
930	>	#endif
931	>
932	>	switch(rnemdFluxType_) {
933	>	case rnemdKE:
934	>	kineticExchange_ += max_val - min_val;
935	>	break;
936	>	case rnemdPx:
937	>	momentumExchange_.x() += max_val - min_val;
938	>	break;
939	>	case rnemdPy:
940	>	momentumExchange_.y() += max_val - min_val;
941	>	break;
942	>	case rnemdPz:
943	>	momentumExchange_.z() += max_val - min_val;
944	>	break;
945	>	default:
946	>	break;
947	>	}
948	>	} else {
949	>	sprintf(painCave.errMsg,
950	>	"RNEMD::doSwap exchange NOT performed because min_val > max_val\n");
951	>	painCave.isFatal = 0;
952	>	painCave.severity = OPENMD_INFO;
953	>	simError();
954	>	failTrialCount_++;
955	>	}
956	>	} else {
957	>	sprintf(painCave.errMsg,
958	>	"RNEMD::doSwap exchange NOT performed because selected object\n"
959	>	"\twas not present in at least one of the two slabs.\n");
960	>	painCave.isFatal = 0;
961	>	painCave.severity = OPENMD_INFO;
962	>	simError();
963	>	failTrialCount_++;
964	>	}
965	>	}
966	>
967	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
968	>	if (!doRNEMD_) return;
969	>	int selei;
970	>	int selej;
971	>
972	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
973	>	RealType time = currentSnap_->getTime();
974	>	Mat3x3d hmat = currentSnap_->getHmat();
975	>
976	>	StuntDouble* sd;
977	>
978	>	vector<StuntDouble*> hotBin, coldBin;
979	>
980	>	RealType Phx = 0.0;
981	>	RealType Phy = 0.0;
982	>	RealType Phz = 0.0;
983	>	RealType Khx = 0.0;
984	>	RealType Khy = 0.0;
985	>	RealType Khz = 0.0;
986	>	RealType Khw = 0.0;
987	>	RealType Pcx = 0.0;
988	>	RealType Pcy = 0.0;
989	>	RealType Pcz = 0.0;
990	>	RealType Kcx = 0.0;
991	>	RealType Kcy = 0.0;
992	>	RealType Kcz = 0.0;
993	>	RealType Kcw = 0.0;
994	>
995	>	for (sd = smanA.beginSelected(selei); sd != NULL;
996	>	sd = smanA.nextSelected(selei)) {
997	>
998	>	Vector3d pos = sd->getPos();
999	>
1000	>	// wrap the stuntdouble's position back into the box:
1001	>
1002	>	if (usePeriodicBoundaryConditions_)
1003	>	currentSnap_->wrapVector(pos);
1004	>
1005	>
1006	>	RealType mass = sd->getMass();
1007	>	Vector3d vel = sd->getVel();
1008	>
1009	>	hotBin.push_back(sd);
1010	>	Phx += mass * vel.x();
1011	>	Phy += mass * vel.y();
1012	>	Phz += mass * vel.z();
1013	>	Khx += mass * vel.x() * vel.x();
1014	>	Khy += mass * vel.y() * vel.y();
1015	>	Khz += mass * vel.z() * vel.z();
1016	>	if (sd->isDirectional()) {
1017	>	Vector3d angMom = sd->getJ();
1018	>	Mat3x3d I = sd->getI();
1019	>	if (sd->isLinear()) {
1020	>	int i = sd->linearAxis();
1021	>	int j = (i + 1) % 3;
1022	>	int k = (i + 2) % 3;
1023	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1024	>	angMom[k] * angMom[k] / I(k, k);
1025	>	} else {
1026	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1027	>	+ angMom[1]*angMom[1]/I(1, 1)
1028	>	+ angMom[2]*angMom[2]/I(2, 2);
1029	>	}
1030	>	}
1031	>	}
1032	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1033	>	sd = smanB.nextSelected(selej)) {
1034	>	Vector3d pos = sd->getPos();
1035	>
1036	>	// wrap the stuntdouble's position back into the box:
1037	>
1038	>	if (usePeriodicBoundaryConditions_)
1039	>	currentSnap_->wrapVector(pos);
1040	>
1041	>	RealType mass = sd->getMass();
1042	>	Vector3d vel = sd->getVel();
1043	>
1044	>	coldBin.push_back(sd);
1045	>	Pcx += mass * vel.x();
1046	>	Pcy += mass * vel.y();
1047	>	Pcz += mass * vel.z();
1048	>	Kcx += mass * vel.x() * vel.x();
1049	>	Kcy += mass * vel.y() * vel.y();
1050	>	Kcz += mass * vel.z() * vel.z();
1051	>	if (sd->isDirectional()) {
1052	>	Vector3d angMom = sd->getJ();
1053	>	Mat3x3d I = sd->getI();
1054	>	if (sd->isLinear()) {
1055	>	int i = sd->linearAxis();
1056	>	int j = (i + 1) % 3;
1057	>	int k = (i + 2) % 3;
1058	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1059	>	angMom[k] * angMom[k] / I(k, k);
1060	>	} else {
1061	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1062	>	+ angMom[1]*angMom[1]/I(1, 1)
1063	>	+ angMom[2]*angMom[2]/I(2, 2);
1064	>	}
1065	>	}
1066	>	}
1067	>
1068	>	Khx *= 0.5;
1069	>	Khy *= 0.5;
1070	>	Khz *= 0.5;
1071	>	Khw *= 0.5;
1072	>	Kcx *= 0.5;
1073	>	Kcy *= 0.5;
1074	>	Kcz *= 0.5;
1075	>	Kcw *= 0.5;
1076	>
1077	>	#ifdef IS_MPI
1078	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phx, 1, MPI::REALTYPE, MPI::SUM);
1079	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phy, 1, MPI::REALTYPE, MPI::SUM);
1080	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Phz, 1, MPI::REALTYPE, MPI::SUM);
1081	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcx, 1, MPI::REALTYPE, MPI::SUM);
1082	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcy, 1, MPI::REALTYPE, MPI::SUM);
1083	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pcz, 1, MPI::REALTYPE, MPI::SUM);
1084	>
1085	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khx, 1, MPI::REALTYPE, MPI::SUM);
1086	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khy, 1, MPI::REALTYPE, MPI::SUM);
1087	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khz, 1, MPI::REALTYPE, MPI::SUM);
1088	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Khw, 1, MPI::REALTYPE, MPI::SUM);
1089	>
1090	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcx, 1, MPI::REALTYPE, MPI::SUM);
1091	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcy, 1, MPI::REALTYPE, MPI::SUM);
1092	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcz, 1, MPI::REALTYPE, MPI::SUM);
1093	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kcw, 1, MPI::REALTYPE, MPI::SUM);
1094	>	#endif
1095	>
1096	>	//solve coldBin coeff's first
1097	>	RealType px = Pcx / Phx;
1098	>	RealType py = Pcy / Phy;
1099	>	RealType pz = Pcz / Phz;
1100	>	RealType c, x, y, z;
1101	>	bool successfulScale = false;
1102	>	if ((rnemdFluxType_ == rnemdFullKE) ||
1103	>	(rnemdFluxType_ == rnemdRotKE)) {
1104	>	//may need sanity check Khw & Kcw > 0
1105	>
1106	>	if (rnemdFluxType_ == rnemdFullKE) {
1107	>	c = 1.0 - kineticTarget_ / (Kcx + Kcy + Kcz + Kcw);
1108	>	} else {
1109	>	c = 1.0 - kineticTarget_ / Kcw;
1110	>	}
1111	>
1112	>	if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1113	>	c = sqrt(c);
1114	>
1115	>	RealType w = 0.0;
1116	>	if (rnemdFluxType_ ==  rnemdFullKE) {
1117	>	x = 1.0 + px * (1.0 - c);
1118	>	y = 1.0 + py * (1.0 - c);
1119	>	z = 1.0 + pz * (1.0 - c);
1120	>	/* more complicated way
1121	>	w = 1.0 + (Kcw - Kcw * c * c - (c * c * (Kcx + Kcy + Kcz
1122	>	+ Khx * px * px + Khy * py * py + Khz * pz * pz)
1123	>	- 2.0 * c * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py)
1124	>	+ Khz * pz * (1.0 + pz)) + Khx * px * (2.0 + px)
1125	>	+ Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1126	>	- Kcx - Kcy - Kcz)) / Khw; the following is simpler
1127	>	*/
1128	>	if ((fabs(x - 1.0) < 0.1) && (fabs(y - 1.0) < 0.1) &&
1129	>	(fabs(z - 1.0) < 0.1)) {
1130	>	w = 1.0 + (kineticTarget_
1131	>	+ Khx * (1.0 - x * x) + Khy * (1.0 - y * y)
1132	>	+ Khz * (1.0 - z * z)) / Khw;
1133	>	}//no need to calculate w if x, y or z is out of range
1134	>	} else {
1135	>	w = 1.0 + kineticTarget_ / Khw;
1136	>	}
1137	>	if ((w > 0.81) && (w < 1.21)) {//restrict scaling coefficients
1138	>	//if w is in the right range, so should be x, y, z.
1139	>	vector<StuntDouble*>::iterator sdi;
1140	>	Vector3d vel;
1141	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1142	>	if (rnemdFluxType_ == rnemdFullKE) {
1143	>	vel = (*sdi)->getVel() * c;
1144	>	(*sdi)->setVel(vel);
1145	>	}
1146	>	if ((*sdi)->isDirectional()) {
1147	>	Vector3d angMom = (*sdi)->getJ() * c;
1148	>	(*sdi)->setJ(angMom);
1149	>	}
1150	>	}
1151	>	w = sqrt(w);
1152	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1153	>	if (rnemdFluxType_ == rnemdFullKE) {
1154	>	vel = (*sdi)->getVel();
1155	>	vel.x() *= x;
1156	>	vel.y() *= y;
1157	>	vel.z() *= z;
1158	>	(*sdi)->setVel(vel);
1159	>	}
1160	>	if ((*sdi)->isDirectional()) {
1161	>	Vector3d angMom = (*sdi)->getJ() * w;
1162	>	(*sdi)->setJ(angMom);
1163	>	}
1164	>	}
1165	>	successfulScale = true;
1166	>	kineticExchange_ += kineticTarget_;
1167	>	}
1168	>	}
1169	>	} else {
1170	>	RealType a000, a110, c0, a001, a111, b01, b11, c1;
1171	>	switch(rnemdFluxType_) {
1172	>	case rnemdKE :
1173	>	/* used hotBin coeff's & only scale x & y dimensions
1174	>	RealType px = Phx / Pcx;
1175	>	RealType py = Phy / Pcy;
1176	>	a110 = Khy;
1177	>	c0 = - Khx - Khy - kineticTarget_;
1178	>	a000 = Khx;
1179	>	a111 = Kcy * py * py;
1180	>	b11 = -2.0 * Kcy * py * (1.0 + py);
1181	>	c1 = Kcy * py * (2.0 + py) + Kcx * px * ( 2.0 + px) + kineticTarget_;
1182	>	b01 = -2.0 * Kcx * px * (1.0 + px);
1183	>	a001 = Kcx * px * px;
1184	>	*/
1185	>	//scale all three dimensions, let c_x = c_y
1186	>	a000 = Kcx + Kcy;
1187	>	a110 = Kcz;
1188	>	c0 = kineticTarget_ - Kcx - Kcy - Kcz;
1189	>	a001 = Khx * px * px + Khy * py * py;
1190	>	a111 = Khz * pz * pz;
1191	>	b01 = -2.0 * (Khx * px * (1.0 + px) + Khy * py * (1.0 + py));
1192	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1193	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1194	>	+ Khz * pz * (2.0 + pz) - kineticTarget_;
1195	>	break;
1196	>	case rnemdPx :
1197	>	c = 1 - momentumTarget_.x() / Pcx;
1198	>	a000 = Kcy;
1199	>	a110 = Kcz;
1200	>	c0 = Kcx * c * c - Kcx - Kcy - Kcz;
1201	>	a001 = py * py * Khy;
1202	>	a111 = pz * pz * Khz;
1203	>	b01 = -2.0 * Khy * py * (1.0 + py);
1204	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1205	>	c1 = Khy * py * (2.0 + py) + Khz * pz * (2.0 + pz)
1206	>	+ Khx * (fastpow(c * px - px - 1.0, 2) - 1.0);
1207	>	break;
1208	>	case rnemdPy :
1209	>	c = 1 - momentumTarget_.y() / Pcy;
1210	>	a000 = Kcx;
1211	>	a110 = Kcz;
1212	>	c0 = Kcy * c * c - Kcx - Kcy - Kcz;
1213	>	a001 = px * px * Khx;
1214	>	a111 = pz * pz * Khz;
1215	>	b01 = -2.0 * Khx * px * (1.0 + px);
1216	>	b11 = -2.0 * Khz * pz * (1.0 + pz);
1217	>	c1 = Khx * px * (2.0 + px) + Khz * pz * (2.0 + pz)
1218	>	+ Khy * (fastpow(c * py - py - 1.0, 2) - 1.0);
1219	>	break;
1220	>	case rnemdPz ://we don't really do this, do we?
1221	>	c = 1 - momentumTarget_.z() / Pcz;
1222	>	a000 = Kcx;
1223	>	a110 = Kcy;
1224	>	c0 = Kcz * c * c - Kcx - Kcy - Kcz;
1225	>	a001 = px * px * Khx;
1226	>	a111 = py * py * Khy;
1227	>	b01 = -2.0 * Khx * px * (1.0 + px);
1228	>	b11 = -2.0 * Khy * py * (1.0 + py);
1229	>	c1 = Khx * px * (2.0 + px) + Khy * py * (2.0 + py)
1230	>	+ Khz * (fastpow(c * pz - pz - 1.0, 2) - 1.0);
1231	>	break;
1232	>	default :
1233	>	break;
1234	>	}
1235	>
1236	>	RealType v1 = a000 * a111 - a001 * a110;
1237	>	RealType v2 = a000 * b01;
1238	>	RealType v3 = a000 * b11;
1239	>	RealType v4 = a000 * c1 - a001 * c0;
1240	>	RealType v8 = a110 * b01;
1241	>	RealType v10 = - b01 * c0;
1242	>
1243	>	RealType u0 = v2 * v10 - v4 * v4;
1244	>	RealType u1 = -2.0 * v3 * v4;
1245	>	RealType u2 = -v2 * v8 - v3 * v3 - 2.0 * v1 * v4;
1246	>	RealType u3 = -2.0 * v1 * v3;
1247	>	RealType u4 = - v1 * v1;
1248	>	//rescale coefficients
1249	>	RealType maxAbs = fabs(u0);
1250	>	if (maxAbs < fabs(u1)) maxAbs = fabs(u1);
1251	>	if (maxAbs < fabs(u2)) maxAbs = fabs(u2);
1252	>	if (maxAbs < fabs(u3)) maxAbs = fabs(u3);
1253	>	if (maxAbs < fabs(u4)) maxAbs = fabs(u4);
1254	>	u0 /= maxAbs;
1255	>	u1 /= maxAbs;
1256	>	u2 /= maxAbs;
1257	>	u3 /= maxAbs;
1258	>	u4 /= maxAbs;
1259	>	//max_element(start, end) is also available.
1260	>	Polynomial<RealType> poly; //same as DoublePolynomial poly;
1261	>	poly.setCoefficient(4, u4);
1262	>	poly.setCoefficient(3, u3);
1263	>	poly.setCoefficient(2, u2);
1264	>	poly.setCoefficient(1, u1);
1265	>	poly.setCoefficient(0, u0);
1266	>	vector<RealType> realRoots = poly.FindRealRoots();
1267	>
1268	>	vector<RealType>::iterator ri;
1269	>	RealType r1, r2, alpha0;
1270	>	vector<pair<RealType,RealType> > rps;
1271	>	for (ri = realRoots.begin(); ri !=realRoots.end(); ri++) {
1272	>	r2 = *ri;
1273	>	//check if FindRealRoots() give the right answer
1274	>	if ( fabs(u0 + r2 * (u1 + r2 * (u2 + r2 * (u3 + r2 * u4)))) > 1e-6 ) {
1275	>	sprintf(painCave.errMsg,
1276	>	"RNEMD Warning: polynomial solve seems to have an error!");
1277	>	painCave.isFatal = 0;
1278	>	simError();
1279	>	failRootCount_++;
1280	>	}
1281	>	//might not be useful w/o rescaling coefficients
1282	>	alpha0 = -c0 - a110 * r2 * r2;
1283	>	if (alpha0 >= 0.0) {
1284	>	r1 = sqrt(alpha0 / a000);
1285	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1286	>	< 1e-6)
1287	>	{ rps.push_back(make_pair(r1, r2)); }
1288	>	if (r1 > 1e-6) { //r1 non-negative
1289	>	r1 = -r1;
1290	>	if (fabs(c1 + r1 * (b01 + r1 * a001) + r2 * (b11 + r2 * a111))
1291	>	< 1e-6)
1292	>	{ rps.push_back(make_pair(r1, r2)); }
1293	>	}
1294	>	}
1295	>	}
1296	>	// Consider combining together the solving pair part w/ the searching
1297	>	// best solution part so that we don't need the pairs vector
1298	>	if (!rps.empty()) {
1299	>	RealType smallestDiff = HONKING_LARGE_VALUE;
1300	>	RealType diff;
1301	>	pair<RealType,RealType> bestPair = make_pair(1.0, 1.0);
1302	>	vector<pair<RealType,RealType> >::iterator rpi;
1303	>	for (rpi = rps.begin(); rpi != rps.end(); rpi++) {
1304	>	r1 = (*rpi).first;
1305	>	r2 = (*rpi).second;
1306	>	switch(rnemdFluxType_) {
1307	>	case rnemdKE :
1308	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1309	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2)
1310	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1311	>	break;
1312	>	case rnemdPx :
1313	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1314	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcy, 2);
1315	>	break;
1316	>	case rnemdPy :
1317	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1318	>	+ fastpow(r1 * r1 / r2 / r2 - Kcz/Kcx, 2);
1319	>	break;
1320	>	case rnemdPz :
1321	>	diff = fastpow(1.0 - r1, 2) + fastpow(1.0 - r2, 2)
1322	>	+ fastpow(r1 * r1 / r2 / r2 - Kcy/Kcx, 2);
1323	>	default :
1324	>	break;
1325	>	}
1326	>	if (diff < smallestDiff) {
1327	>	smallestDiff = diff;
1328	>	bestPair = *rpi;
1329	>	}
1330	>	}
1331	>	#ifdef IS_MPI
1332	>	if (worldRank == 0) {
1333	>	#endif
1334	>	// sprintf(painCave.errMsg,
1335	>	//         "RNEMD: roots r1= %lf\tr2 = %lf\n",
1336	>	//         bestPair.first, bestPair.second);
1337	>	// painCave.isFatal = 0;
1338	>	// painCave.severity = OPENMD_INFO;
1339	>	// simError();
1340	>	#ifdef IS_MPI
1341	>	}
1342	>	#endif
1343	>
1344	>	switch(rnemdFluxType_) {
1345	>	case rnemdKE :
1346	>	x = bestPair.first;
1347	>	y = bestPair.first;
1348	>	z = bestPair.second;
1349	>	break;
1350	>	case rnemdPx :
1351	>	x = c;
1352	>	y = bestPair.first;
1353	>	z = bestPair.second;
1354	>	break;
1355	>	case rnemdPy :
1356	>	x = bestPair.first;
1357	>	y = c;
1358	>	z = bestPair.second;
1359	>	break;
1360	>	case rnemdPz :
1361	>	x = bestPair.first;
1362	>	y = bestPair.second;
1363	>	z = c;
1364	>	break;
1365	>	default :
1366	>	break;
1367	>	}
1368	>	vector<StuntDouble*>::iterator sdi;
1369	>	Vector3d vel;
1370	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1371	>	vel = (*sdi)->getVel();
1372	>	vel.x() *= x;
1373	>	vel.y() *= y;
1374	>	vel.z() *= z;
1375	>	(*sdi)->setVel(vel);
1376	>	}
1377	>	//convert to hotBin coefficient
1378	>	x = 1.0 + px * (1.0 - x);
1379	>	y = 1.0 + py * (1.0 - y);
1380	>	z = 1.0 + pz * (1.0 - z);
1381	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1382	>	vel = (*sdi)->getVel();
1383	>	vel.x() *= x;
1384	>	vel.y() *= y;
1385	>	vel.z() *= z;
1386	>	(*sdi)->setVel(vel);
1387	>	}
1388	>	successfulScale = true;
1389	>	switch(rnemdFluxType_) {
1390	>	case rnemdKE :
1391	>	kineticExchange_ += kineticTarget_;
1392	>	break;
1393	>	case rnemdPx :
1394	>	case rnemdPy :
1395	>	case rnemdPz :
1396	>	momentumExchange_ += momentumTarget_;
1397	>	break;
1398	>	default :
1399	>	break;
1400	>	}
1401	>	}
1402	>	}
1403	>	if (successfulScale != true) {
1404	>	sprintf(painCave.errMsg,
1405	>	"RNEMD::doNIVS exchange NOT performed - roots that solve\n"
1406	>	"\tthe constraint equations may not exist or there may be\n"
1407	>	"\tno selected objects in one or both slabs.\n");
1408	>	painCave.isFatal = 0;
1409	>	painCave.severity = OPENMD_INFO;
1410	>	simError();
1411	>	failTrialCount_++;
1412	>	}
1413	>	}
1414	>
1415	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1416	>	if (!doRNEMD_) return;
1417	>	int selei;
1418	>	int selej;
1419	>
1420	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1421	>	RealType time = currentSnap_->getTime();
1422	>	Mat3x3d hmat = currentSnap_->getHmat();
1423	>
1424	>	StuntDouble* sd;
1425	>
1426	>	vector<StuntDouble*> hotBin, coldBin;
1427	>
1428	>	Vector3d Ph(V3Zero);
1429	>	Vector3d Lh(V3Zero);
1430	>	RealType Mh = 0.0;
1431	>	Mat3x3d Ih(0.0);
1432	>	RealType Kh = 0.0;
1433	>	Vector3d Pc(V3Zero);
1434	>	Vector3d Lc(V3Zero);
1435	>	RealType Mc = 0.0;
1436	>	Mat3x3d Ic(0.0);
1437	>	RealType Kc = 0.0;
1438	>
1439	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1440	>	sd = smanA.nextSelected(selei)) {
1441	>
1442	>	Vector3d pos = sd->getPos();
1443	>
1444	>	// wrap the stuntdouble's position back into the box:
1445	>
1446	>	if (usePeriodicBoundaryConditions_)
1447	>	currentSnap_->wrapVector(pos);
1448	>
1449	>	RealType mass = sd->getMass();
1450	>	Vector3d vel = sd->getVel();
1451	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1452	>	RealType r2;
1453	>
1454	>	hotBin.push_back(sd);
1455	>	Ph += mass * vel;
1456	>	Mh += mass;
1457	>	Kh += mass * vel.lengthSquare();
1458	>	Lh += mass * cross(rPos, vel);
1459	>	Ih -= outProduct(rPos, rPos) * mass;
1460	>	r2 = rPos.lengthSquare();
1461	>	Ih(0, 0) += mass * r2;
1462	>	Ih(1, 1) += mass * r2;
1463	>	Ih(2, 2) += mass * r2;
1464	>
1465	>	if (rnemdFluxType_ == rnemdFullKE) {
1466	>	if (sd->isDirectional()) {
1467	>	Vector3d angMom = sd->getJ();
1468	>	Mat3x3d I = sd->getI();
1469	>	if (sd->isLinear()) {
1470	>	int i = sd->linearAxis();
1471	>	int j = (i + 1) % 3;
1472	>	int k = (i + 2) % 3;
1473	>	Kh += angMom[j] * angMom[j] / I(j, j) +
1474	>	angMom[k] * angMom[k] / I(k, k);
1475	>	} else {
1476	>	Kh += angMom[0] * angMom[0] / I(0, 0) +
1477	>	angMom[1] * angMom[1] / I(1, 1) +
1478	>	angMom[2] * angMom[2] / I(2, 2);
1479	>	}
1480	>	}
1481	>	}
1482	>	}
1483	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1484	>	sd = smanB.nextSelected(selej)) {
1485	>
1486	>	Vector3d pos = sd->getPos();
1487	>
1488	>	// wrap the stuntdouble's position back into the box:
1489	>
1490	>	if (usePeriodicBoundaryConditions_)
1491	>	currentSnap_->wrapVector(pos);
1492	>
1493	>	RealType mass = sd->getMass();
1494	>	Vector3d vel = sd->getVel();
1495	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1496	>	RealType r2;
1497	>
1498	>	coldBin.push_back(sd);
1499	>	Pc += mass * vel;
1500	>	Mc += mass;
1501	>	Kc += mass * vel.lengthSquare();
1502	>	Lc += mass * cross(rPos, vel);
1503	>	Ic -= outProduct(rPos, rPos) * mass;
1504	>	r2 = rPos.lengthSquare();
1505	>	Ic(0, 0) += mass * r2;
1506	>	Ic(1, 1) += mass * r2;
1507	>	Ic(2, 2) += mass * r2;
1508	>
1509	>	if (rnemdFluxType_ == rnemdFullKE) {
1510	>	if (sd->isDirectional()) {
1511	>	Vector3d angMom = sd->getJ();
1512	>	Mat3x3d I = sd->getI();
1513	>	if (sd->isLinear()) {
1514	>	int i = sd->linearAxis();
1515	>	int j = (i + 1) % 3;
1516	>	int k = (i + 2) % 3;
1517	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1518	>	angMom[k] * angMom[k] / I(k, k);
1519	>	} else {
1520	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1521	>	angMom[1] * angMom[1] / I(1, 1) +
1522	>	angMom[2] * angMom[2] / I(2, 2);
1523	>	}
1524	>	}
1525	>	}
1526	>	}
1527	>
1528	>	Kh *= 0.5;
1529	>	Kc *= 0.5;
1530	>
1531	>	#ifdef IS_MPI
1532	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1533	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1534	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1535	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1536	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1537	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1538	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1539	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1540	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1541	>	MPI::REALTYPE, MPI::SUM);
1542	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1543	>	MPI::REALTYPE, MPI::SUM);
1544	>	#endif
1545	>
1546	>	bool successfulExchange = false;
1547	>	if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1548	>	Vector3d vc = Pc / Mc;
1549	>	Vector3d ac = -momentumTarget_ / Mc + vc;
1550	>	Vector3d acrec = -momentumTarget_ / Mc;
1551	>
1552	>	// We now need the inverse of the inertia tensor to calculate the
1553	>	// angular velocity of the cold slab;
1554	>	Mat3x3d Ici = Ic.inverse();
1555	>	Vector3d omegac = Ici * Lc;
1556	>	Vector3d bc  = -(Ici * angularMomentumTarget_) + omegac;
1557	>	Vector3d bcrec = bc - omegac;
1558	>
1559	>	RealType cNumerator = Kc - kineticTarget_
1560	>	- 0.5 * Mc * ac.lengthSquare() - 0.5 * ( dot(bc, Ic * bc));
1561	>	if (cNumerator > 0.0) {
1562	>
1563	>	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare()
1564	>	- 0.5*(dot(omegac, Ic * omegac));
1565	>
1566	>	if (cDenominator > 0.0) {
1567	>	RealType c = sqrt(cNumerator / cDenominator);
1568	>	if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1569	>
1570	>	Vector3d vh = Ph / Mh;
1571	>	Vector3d ah = momentumTarget_ / Mh + vh;
1572	>	Vector3d ahrec = momentumTarget_ / Mh;
1573	>
1574	>	// We now need the inverse of the inertia tensor to
1575	>	// calculate the angular velocity of the hot slab;
1576	>	Mat3x3d Ihi = Ih.inverse();
1577	>	Vector3d omegah = Ihi * Lh;
1578	>	Vector3d bh  = (Ihi * angularMomentumTarget_) + omegah;
1579	>	Vector3d bhrec = bh - omegah;
1580	>
1581	>	RealType hNumerator = Kh + kineticTarget_
1582	>	- 0.5 * Mh * ah.lengthSquare() - 0.5 * ( dot(bh, Ih * bh));;
1583	>	if (hNumerator > 0.0) {
1584	>
1585	>	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare()
1586	>	- 0.5*(dot(omegah, Ih * omegah));
1587	>
1588	>	if (hDenominator > 0.0) {
1589	>	RealType h = sqrt(hNumerator / hDenominator);
1590	>	if ((h > 0.9) && (h < 1.1)) {
1591	>
1592	>	vector<StuntDouble*>::iterator sdi;
1593	>	Vector3d vel;
1594	>	Vector3d rPos;
1595	>
1596	>	for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1597	>	//vel = (*sdi)->getVel();
1598	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1599	>	vel = ((*sdi)->getVel() - vc - cross(omegac, rPos)) * c
1600	>	+ ac + cross(bc, rPos);
1601	>	(*sdi)->setVel(vel);
1602	>	if (rnemdFluxType_ == rnemdFullKE) {
1603	>	if ((*sdi)->isDirectional()) {
1604	>	Vector3d angMom = (*sdi)->getJ() * c;
1605	>	(*sdi)->setJ(angMom);
1606	>	}
1607	>	}
1608	>	}
1609	>	for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1610	>	//vel = (*sdi)->getVel();
1611	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1612	>	vel = ((*sdi)->getVel() - vh - cross(omegah, rPos)) * h
1613	>	+ ah + cross(bh, rPos);
1614	>	(*sdi)->setVel(vel);
1615	>	if (rnemdFluxType_ == rnemdFullKE) {
1616	>	if ((*sdi)->isDirectional()) {
1617	>	Vector3d angMom = (*sdi)->getJ() * h;
1618	>	(*sdi)->setJ(angMom);
1619	>	}
1620	>	}
1621	>	}
1622	>	successfulExchange = true;
1623	>	kineticExchange_ += kineticTarget_;
1624	>	momentumExchange_ += momentumTarget_;
1625	>	angularMomentumExchange_ += angularMomentumTarget_;
1626	>	}
1627	>	}
1628	>	}
1629	>	}
1630	>	}
1631	>	}
1632	>	}
1633	>	if (successfulExchange != true) {
1634	>	sprintf(painCave.errMsg,
1635	>	"RNEMD::doVSS exchange NOT performed - roots that solve\n"
1636	>	"\tthe constraint equations may not exist or there may be\n"
1637	>	"\tno selected objects in one or both slabs.\n");
1638	>	painCave.isFatal = 0;
1639	>	painCave.severity = OPENMD_INFO;
1640	>	simError();
1641	>	failTrialCount_++;
1642	>	}
1643	>	}
1644	>
1645	>	RealType RNEMD::getDividingArea() {
1646	>
1647	>	if (hasDividingArea_) return dividingArea_;
1648	>
1649	>	RealType areaA, areaB;
1650	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1651	>
1652	>	if (hasSelectionA_) {
1653	>	int isd;
1654	>	StuntDouble* sd;
1655	>	vector<StuntDouble*> aSites;
1656	>	ConvexHull* surfaceMeshA = new ConvexHull();
1657	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1658	>	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1659	>	sd = seleManA_.nextSelected(isd)) {
1660	>	aSites.push_back(sd);
1661	>	}
1662	>	surfaceMeshA->computeHull(aSites);
1663	>	areaA = surfaceMeshA->getArea();
1664	>	} else {
1665	>	if (usePeriodicBoundaryConditions_) {
1666	>	// in periodic boundaries, the surface area is twice the x-y
1667	>	// area of the current box:
1668	>	areaA = 2.0 * snap->getXYarea();
1669	>	} else {
1670	>	// in non-periodic simulations, without explicitly setting
1671	>	// selections, the sphere radius sets the surface area of the
1672	>	// dividing surface:
1673	>	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1674	>	}
1675	>	}
1676	>
1677	>	if (hasSelectionB_) {
1678	>	int isd;
1679	>	StuntDouble* sd;
1680	>	vector<StuntDouble*> bSites;
1681	>	ConvexHull* surfaceMeshB = new ConvexHull();
1682	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1683	>	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1684	>	sd = seleManB_.nextSelected(isd)) {
1685	>	bSites.push_back(sd);
1686	>	}
1687	>	surfaceMeshB->computeHull(bSites);
1688	>	areaB = surfaceMeshB->getArea();
1689	>	} else {
1690	>	if (usePeriodicBoundaryConditions_) {
1691	>	// in periodic boundaries, the surface area is twice the x-y
1692	>	// area of the current box:
1693	>	areaB = 2.0 * snap->getXYarea();
1694	>	} else {
1695	>	// in non-periodic simulations, without explicitly setting
1696	>	// selections, but if a sphereBradius has been set, just use that:
1697	>	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1698	>	}
1699	>	}
1700	>
1701	>	dividingArea_ = min(areaA, areaB);
1702	>	hasDividingArea_ = true;
1703	>	return dividingArea_;
1704	>	}
1705	>
1706	>	void RNEMD::doRNEMD() {
1707	>	if (!doRNEMD_) return;
1708	>	trialCount_++;
1709	>
1710	>	// object evaluator:
1711	>	evaluator_.loadScriptString(rnemdObjectSelection_);
1712	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1713	>
1714	>	evaluatorA_.loadScriptString(selectionA_);
1715	>	evaluatorB_.loadScriptString(selectionB_);
1716	>
1717	>	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1718	>	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1719	>
1720	>	commonA_ = seleManA_ & seleMan_;
1721	>	commonB_ = seleManB_ & seleMan_;
1722	>
1723	>	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1724	>	// dt = exchange time interval
1725	>	// flux = target flux
1726	>	// dividingArea = smallest dividing surface between the two regions
1727	>
1728	>	hasDividingArea_ = false;
1729	>	RealType area = getDividingArea();
1730	>
1731	>	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1732	>	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1733	>	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1734	>
1735	>	switch(rnemdMethod_) {
1736	>	case rnemdSwap:
1737	>	doSwap(commonA_, commonB_);
1738	>	break;
1739	>	case rnemdNIVS:
1740	>	doNIVS(commonA_, commonB_);
1741	>	break;
1742	>	case rnemdVSS:
1743	>	doVSS(commonA_, commonB_);
1744	>	break;
1745	>	case rnemdUnkownMethod:
1746	>	default :
1747	>	break;
1748	>	}
1749	>	}
1750	>
1751	>	void RNEMD::collectData() {
1752	>	if (!doRNEMD_) return;
1753	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1754	>
1755	>	// collectData can be called more frequently than the doRNEMD, so use the
1756	>	// computed area from the last exchange time:
1757	>
1758	>	areaAccumulator_->add(getDividingArea());
1759	>	Mat3x3d hmat = currentSnap_->getHmat();
1760	>	seleMan_.setSelectionSet(evaluator_.evaluate());
1761	>
1762	>	int selei(0);
1763	>	StuntDouble* sd;
1764	>	int binNo;
1765	>
1766	>	vector<RealType> binMass(nBins_, 0.0);
1767	>	vector<RealType> binPx(nBins_, 0.0);
1768	>	vector<RealType> binPy(nBins_, 0.0);
1769	>	vector<RealType> binPz(nBins_, 0.0);
1770	>	vector<RealType> binOmegax(nBins_, 0.0);
1771	>	vector<RealType> binOmegay(nBins_, 0.0);
1772	>	vector<RealType> binOmegaz(nBins_, 0.0);
1773	>	vector<RealType> binKE(nBins_, 0.0);
1774	>	vector<int> binDOF(nBins_, 0);
1775	>	vector<int> binCount(nBins_, 0);
1776	>
1777	>	// alternative approach, track all molecules instead of only those
1778	>	// selected for scaling/swapping:
1779	>	/*
1780	>	SimInfo::MoleculeIterator miter;
1781	>	vector<StuntDouble*>::iterator iiter;
1782	>	Molecule* mol;
1783	>	StuntDouble* sd;
1784	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1785	>	mol = info_->nextMolecule(miter))
1786	>	sd is essentially sd
1787	>	for (sd = mol->beginIntegrableObject(iiter);
1788	>	sd != NULL;
1789	>	sd = mol->nextIntegrableObject(iiter))
1790	>	*/
1791	>
1792	>	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1793	>	sd = seleMan_.nextSelected(selei)) {
1794	>
1795	>	Vector3d pos = sd->getPos();
1796	>
1797	>	// wrap the stuntdouble's position back into the box:
1798	>
1799	>	if (usePeriodicBoundaryConditions_) {
1800	>	currentSnap_->wrapVector(pos);
1801	>	// which bin is this stuntdouble in?
1802	>	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1803	>	// Shift molecules by half a box to have bins start at 0
1804	>	// The modulo operator is used to wrap the case when we are
1805	>	// beyond the end of the bins back to the beginning.
1806	>	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1807	>	} else {
1808	>	Vector3d rPos = pos - coordinateOrigin_;
1809	>	binNo = int(rPos.length() / binWidth_);
1810	>	}
1811	>
1812	>	RealType mass = sd->getMass();
1813	>	Vector3d vel = sd->getVel();
1814	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1815	>	Vector3d aVel = cross(rPos, vel);
1816	>
1817	>	if (binNo < nBins_)  {
1818	>	binCount[binNo]++;
1819	>	binMass[binNo] += mass;
1820	>	binPx[binNo] += mass*vel.x();
1821	>	binPy[binNo] += mass*vel.y();
1822	>	binPz[binNo] += mass*vel.z();
1823	>	binOmegax[binNo] += aVel.x();
1824	>	binOmegay[binNo] += aVel.y();
1825	>	binOmegaz[binNo] += aVel.z();
1826	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1827	>	binDOF[binNo] += 3;
1828	>
1829	>	if (sd->isDirectional()) {
1830	>	Vector3d angMom = sd->getJ();
1831	>	Mat3x3d I = sd->getI();
1832	>	if (sd->isLinear()) {
1833	>	int i = sd->linearAxis();
1834	>	int j = (i + 1) % 3;
1835	>	int k = (i + 2) % 3;
1836	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1837	>	angMom[k] * angMom[k] / I(k, k));
1838	>	binDOF[binNo] += 2;
1839	>	} else {
1840	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1841	>	angMom[1] * angMom[1] / I(1, 1) +
1842	>	angMom[2] * angMom[2] / I(2, 2));
1843	>	binDOF[binNo] += 3;
1844	>	}
1845	>	}
1846	>	}
1847	>	}
1848	>
1849	>	#ifdef IS_MPI
1850	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1851	>	nBins_, MPI::INT, MPI::SUM);
1852	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binMass[0],
1853	>	nBins_, MPI::REALTYPE, MPI::SUM);
1854	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPx[0],
1855	>	nBins_, MPI::REALTYPE, MPI::SUM);
1856	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPy[0],
1857	>	nBins_, MPI::REALTYPE, MPI::SUM);
1858	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1859	>	nBins_, MPI::REALTYPE, MPI::SUM);
1860	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1861	>	nBins_, MPI::REALTYPE, MPI::SUM);
1862	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1863	>	nBins_, MPI::REALTYPE, MPI::SUM);
1864	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1865	>	nBins_, MPI::REALTYPE, MPI::SUM);
1866	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1867	>	nBins_, MPI::REALTYPE, MPI::SUM);
1868	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
1869	>	nBins_, MPI::INT, MPI::SUM);
1870	>	#endif
1871	>
1872	>	Vector3d vel;
1873	>	Vector3d aVel;
1874	>	RealType den;
1875	>	RealType temp;
1876	>	RealType z;
1877	>	RealType r;
1878	>	for (int i = 0; i < nBins_; i++) {
1879	>	if (usePeriodicBoundaryConditions_) {
1880	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1881	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1882	>	/ currentSnap_->getVolume() ;
1883	>	} else {
1884	>	r = (((RealType)i + 0.5) * binWidth_);
1885	>	RealType rinner = (RealType)i * binWidth_;
1886	>	RealType router = (RealType)(i+1) * binWidth_;
1887	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1888	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1889	>	}
1890	>	vel.x() = binPx[i] / binMass[i];
1891	>	vel.y() = binPy[i] / binMass[i];
1892	>	vel.z() = binPz[i] / binMass[i];
1893	>	aVel.x() = binOmegax[i];
1894	>	aVel.y() = binOmegay[i];
1895	>	aVel.z() = binOmegaz[i];
1896	>
1897	>	if (binCount[i] > 0) {
1898	>	// only add values if there are things to add
1899	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1900	>	PhysicalConstants::energyConvert);
1901	>
1902	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1903	>	if(outputMask_[j]) {
1904	>	switch(j) {
1905	>	case Z:
1906	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1907	>	break;
1908	>	case R:
1909	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1910	>	break;
1911	>	case TEMPERATURE:
1912	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1913	>	break;
1914	>	case VELOCITY:
1915	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1916	>	break;
1917	>	case ANGULARVELOCITY:
1918	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
1919	>	break;
1920	>	case DENSITY:
1921	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
1922	>	break;
1923	>	}
1924	>	}
1925	>	}
1926	>	}
1927	>	}
1928	>	}
1929	>
1930	>	void RNEMD::getStarted() {
1931	>	if (!doRNEMD_) return;
1932	>	hasDividingArea_ = false;
1933	>	collectData();
1934	>	writeOutputFile();
1935	>	}
1936	>
1937	>	void RNEMD::parseOutputFileFormat(const std::string& format) {
1938	>	if (!doRNEMD_) return;
1939	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
1940	>
1941	>	while(tokenizer.hasMoreTokens()) {
1942	>	std::string token(tokenizer.nextToken());
1943	>	toUpper(token);
1944	>	OutputMapType::iterator i = outputMap_.find(token);
1945	>	if (i != outputMap_.end()) {
1946	>	outputMask_.set(i->second);
1947	>	} else {
1948	>	sprintf( painCave.errMsg,
1949	>	"RNEMD::parseOutputFileFormat: %s is not a recognized\n"
1950	>	"\toutputFileFormat keyword.\n", token.c_str() );
1951	>	painCave.isFatal = 0;
1952	>	painCave.severity = OPENMD_ERROR;
1953	>	simError();
1954	>	}
1955	>	}
1956	>	}
1957	>
1958	>	void RNEMD::writeOutputFile() {
1959	>	if (!doRNEMD_) return;
1960	>
1961	>	#ifdef IS_MPI
1962	>	// If we're the root node, should we print out the results
1963	>	int worldRank = MPI::COMM_WORLD.Get_rank();
1964	>	if (worldRank == 0) {
1965	>	#endif
1966	>	rnemdFile_.open(rnemdFileName_.c_str(), std::ios::out | std::ios::trunc );
1967	>
1968	>	if( !rnemdFile_ ){
1969	>	sprintf( painCave.errMsg,
1970	>	"Could not open \"%s\" for RNEMD output.\n",
1971	>	rnemdFileName_.c_str());
1972	>	painCave.isFatal = 1;
1973	>	simError();
1974	>	}
1975	>
1976	>	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1977	>
1978	>	RealType time = currentSnap_->getTime();
1979	>	RealType avgArea;
1980	>	areaAccumulator_->getAverage(avgArea);
1981	>	RealType Jz = kineticExchange_ / (time * avgArea)
1982	>	/ PhysicalConstants::energyConvert;
1983	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
1984	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
1985	>
1986	>	rnemdFile_ << "#######################################################\n";
1987	>	rnemdFile_ << "# RNEMD {\n";
1988	>
1989	>	map<string, RNEMDMethod>::iterator mi;
1990	>	for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
1991	>	if ( (*mi).second == rnemdMethod_)
1992	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
1993	>	}
1994	>	map<string, RNEMDFluxType>::iterator fi;
1995	>	for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
1996	>	if ( (*fi).second == rnemdFluxType_)
1997	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
1998	>	}
1999	>
2000	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2001	>
2002	>	rnemdFile_ << "#    objectSelection = \""
2003	>	<< rnemdObjectSelection_ << "\";\n";
2004	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2005	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2006	>	rnemdFile_ << "# }\n";
2007	>	rnemdFile_ << "#######################################################\n";
2008	>	rnemdFile_ << "# RNEMD report:\n";
2009	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2010	>	rnemdFile_ << "# Target flux:\n";
2011	>	rnemdFile_ << "#           kinetic = "
2012	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2013	>	<< " (kcal/mol/A^2/fs)\n";
2014	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2015	>	<< " (amu/A/fs^2)\n";
2016	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2017	>	<< " (amu/A^2/fs^2)\n";
2018	>	rnemdFile_ << "# Target one-time exchanges:\n";
2019	>	rnemdFile_ << "#          kinetic = "
2020	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2021	>	<< " (kcal/mol)\n";
2022	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2023	>	<< " (amu*A/fs)\n";
2024	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2025	>	<< " (amu*A^2/fs)\n";
2026	>	rnemdFile_ << "# Actual exchange totals:\n";
2027	>	rnemdFile_ << "#          kinetic = "
2028	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2029	>	<< " (kcal/mol)\n";
2030	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2031	>	<< " (amu*A/fs)\n";
2032	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2033	>	<< " (amu*A^2/fs)\n";
2034	>	rnemdFile_ << "# Actual flux:\n";
2035	>	rnemdFile_ << "#          kinetic = " << Jz
2036	>	<< " (kcal/mol/A^2/fs)\n";
2037	>	rnemdFile_ << "#          momentum = " << JzP
2038	>	<< " (amu/A/fs^2)\n";
2039	>	rnemdFile_ << "#  angular momentum = " << JzL
2040	>	<< " (amu/A^2/fs^2)\n";
2041	>	rnemdFile_ << "# Exchange statistics:\n";
2042	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2043	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2044	>	if (rnemdMethod_ == rnemdNIVS) {
2045	>	rnemdFile_ << "#  NIVS root-check errors = "
2046	>	<< failRootCount_ << "\n";
2047	>	}
2048	>	rnemdFile_ << "#######################################################\n";
2049	>
2050	>
2051	>
2052	>	//write title
2053	>	rnemdFile_ << "#";
2054	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2055	>	if (outputMask_[i]) {
2056	>	rnemdFile_ << "\t" << data_[i].title <<
2057	>	"(" << data_[i].units << ")";
2058	>	// add some extra tabs for column alignment
2059	>	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2060	>	}
2061	>	}
2062	>	rnemdFile_ << std::endl;
2063	>
2064	>	rnemdFile_.precision(8);
2065	>
2066	>	for (int j = 0; j < nBins_; j++) {
2067	>
2068	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2069	>	if (outputMask_[i]) {
2070	>	if (data_[i].dataType == "RealType")
2071	>	writeReal(i,j);
2072	>	else if (data_[i].dataType == "Vector3d")
2073	>	writeVector(i,j);
2074	>	else {
2075	>	sprintf( painCave.errMsg,
2076	>	"RNEMD found an unknown data type for: %s ",
2077	>	data_[i].title.c_str());
2078	>	painCave.isFatal = 1;
2079	>	simError();
2080	>	}
2081	>	}
2082	>	}
2083	>	rnemdFile_ << std::endl;
2084	>
2085	>	}
2086	>
2087	>	rnemdFile_ << "#######################################################\n";
2088	>	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2089	>	rnemdFile_ << "#######################################################\n";
2090	>
2091	>
2092	>	for (int j = 0; j < nBins_; j++) {
2093	>	rnemdFile_ << "#";
2094	>	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2095	>	if (outputMask_[i]) {
2096	>	if (data_[i].dataType == "RealType")
2097	>	writeRealStdDev(i,j);
2098	>	else if (data_[i].dataType == "Vector3d")
2099	>	writeVectorStdDev(i,j);
2100	>	else {
2101	>	sprintf( painCave.errMsg,
2102	>	"RNEMD found an unknown data type for: %s ",
2103	>	data_[i].title.c_str());
2104	>	painCave.isFatal = 1;
2105	>	simError();
2106	>	}
2107	>	}
2108	>	}
2109	>	rnemdFile_ << std::endl;
2110	>
2111	>	}
2112	>
2113	>	rnemdFile_.flush();
2114	>	rnemdFile_.close();
2115	>
2116	>	#ifdef IS_MPI
2117	>	}
2118	>	#endif
2119	>
2120	>	}
2121	>
2122	>	void RNEMD::writeReal(int index, unsigned int bin) {
2123	>	if (!doRNEMD_) return;
2124	>	assert(index >=0 && index < ENDINDEX);
2125	>	assert(int(bin) < nBins_);
2126	>	RealType s;
2127	>	int count;
2128	>
2129	>	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2130	>	if (count == 0) return;
2131	>
2132	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2133	>
2134	>	if (! isinf(s) && ! isnan(s)) {
2135	>	rnemdFile_ << "\t" << s;
2136	>	} else{
2137	>	sprintf( painCave.errMsg,
2138	>	"RNEMD detected a numerical error writing: %s for bin %d",
2139	>	data_[index].title.c_str(), bin);
2140	>	painCave.isFatal = 1;
2141	>	simError();
2142	>	}
2143	>	}
2144	>
2145	>	void RNEMD::writeVector(int index, unsigned int bin) {
2146	>	if (!doRNEMD_) return;
2147	>	assert(index >=0 && index < ENDINDEX);
2148	>	assert(int(bin) < nBins_);
2149	>	Vector3d s;
2150	>	int count;
2151	>
2152	>	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2153	>	if (count == 0) return;
2154	>
2155	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2156	>	if (isinf(s[0]) || isnan(s[0]) ||
2157	>	isinf(s[1]) || isnan(s[1]) ||
2158	>	isinf(s[2]) || isnan(s[2]) ) {
2159	>	sprintf( painCave.errMsg,
2160	>	"RNEMD detected a numerical error writing: %s for bin %d",
2161	>	data_[index].title.c_str(), bin);
2162	>	painCave.isFatal = 1;
2163	>	simError();
2164	>	} else {
2165	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2166	>	}
2167	>	}
2168	>
2169	>	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2170	>	if (!doRNEMD_) return;
2171	>	assert(index >=0 && index < ENDINDEX);
2172	>	assert(int(bin) < nBins_);
2173	>	RealType s;
2174	>	int count;
2175	>
2176	>	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2177	>	if (count == 0) return;
2178	>
2179	>	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2180	>
2181	>	if (! isinf(s) && ! isnan(s)) {
2182	>	rnemdFile_ << "\t" << s;
2183	>	} else{
2184	>	sprintf( painCave.errMsg,
2185	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2186	>	data_[index].title.c_str(), bin);
2187	>	painCave.isFatal = 1;
2188	>	simError();
2189	>	}
2190	>	}
2191	>
2192	>	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2193	>	if (!doRNEMD_) return;
2194	>	assert(index >=0 && index < ENDINDEX);
2195	>	assert(int(bin) < nBins_);
2196	>	Vector3d s;
2197	>	int count;
2198	>
2199	>	count = dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->count();
2200	>	if (count == 0) return;
2201	>
2202	>	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2203	>	if (isinf(s[0]) || isnan(s[0]) ||
2204	>	isinf(s[1]) || isnan(s[1]) ||
2205	>	isinf(s[2]) || isnan(s[2]) ) {
2206	>	sprintf( painCave.errMsg,
2207	>	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2208	>	data_[index].title.c_str(), bin);
2209	>	painCave.isFatal = 1;
2210	>	simError();
2211	>	} else {
2212	>	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2213	>	}
2214	>	}
2215	>	}
2216	>

Comparing:
trunk/src/integrators/RNEMD.cpp (property svn:keywords), Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (property svn:keywords), Revision 1854 by gezelter, Thu Mar 28 20:54:06 2013 UTC

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